Mercurial > repos > iuc > mothur_sub_sample

comparison sub.sample.xml @ 1:f18e9f139d14 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:44:02 -0400
parents 8ccebd04ca3d
children 1f5904c5ee42
comparison
equal deleted inserted replaced
0:8ccebd04ca3d 1:f18e9f139d14
2 <description>Create a sub sample</description> 2 <description>Create a sub sample</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$input.otu" input_otu.dat && 13 ln -s "$input.otu" input_otu.dat &&
11 ln -s "$count" count.dat && 14 ln -s "$count" count.dat &&
12 ln -s "$taxonomy" taxonomy.dat && 15 ln -s "$taxonomy" taxonomy.dat &&
13 #if $input.format == "fasta": 16 #if $input.format == "fasta":
59 ,size=$size 62 ,size=$size
60 #end if 63 #end if
61 )' 64 )'
62 | sed 's/ //g' ## mothur trips over whitespace 65 | sed 's/ //g' ## mothur trips over whitespace
63 | mothur 66 | mothur
67 | tee mothur.out.log
64 ]]></command> 68 ]]></command>
65 <inputs> 69 <inputs>
66 <conditional name="input"> 70 <conditional name="input">
67 <param name="format" type="select" label="Select type of data to sub sample"> 71 <param name="format" type="select" label="Select type of data to sub sample">
68 <option value="fasta">FASTA</option> 72 <option value="fasta">FASTA</option>
137 </param> 141 </param>
138 </when> 142 </when>
139 </conditional> 143 </conditional>
140 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/> 144 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
141 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 145 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
142 <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/> 146 <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
143 </inputs> 147 </inputs>
144 <outputs> 148 <outputs>
145 <expand macro="logfile-output"/> 149 <expand macro="logfile-output"/>
146 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta"> 150 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
147 <filter>input['format'] == 'fasta'</filter> 151 <filter>input['format'] == 'fasta'</filter>
152 </data>
153 <data name="taxonomy_out" format_source="taxonomy" from_work_dir="taxonomy.subsample.dat" label="${tool.name} on ${on_string}: subsample.taxonomy">
154 <filter>taxonomy</filter>
148 </data> 155 </data>
149 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list"> 156 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list">
150 <filter>input['format'] == 'list'</filter> 157 <filter>input['format'] == 'list'</filter>
151 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.list"/> 158 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.list"/>
152 </collection> 159 </collection>
196 </assert_contents> 203 </assert_contents>
197 </element> 204 </element>
198 </output_collection> 205 </output_collection>
199 <expand macro="logfile-test"/> 206 <expand macro="logfile-test"/>
200 </test> 207 </test>
201 <test><!-- test with fasta --> 208 <test><!-- test with fasta and taxonomy -->
202 <param name="format" value="fasta"/> 209 <param name="format" value="fasta"/>
203 <param name="otu" value="amazon.fasta" ftype="fasta"/> 210 <param name="otu" value="amazon.fasta" ftype="fasta"/>
211 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
204 <output name="fasta_out" ftype="fasta"> 212 <output name="fasta_out" ftype="fasta">
205 <assert_contents> 213 <assert_contents>
206 <has_text text=">U"/> 214 <has_text text=">U"/>
215 </assert_contents>
216 </output>
217 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
218 <assert_contents>
219 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
207 </assert_contents> 220 </assert_contents>
208 </output> 221 </output>
209 <expand macro="logfile-test"/> 222 <expand macro="logfile-test"/>
210 </test> 223 </test>
211 <test><!-- test with fasta and group file and name file --> 224 <test><!-- test with fasta and group file and name file -->
275 <help> 288 <help>
276 <![CDATA[ 289 <![CDATA[
277 290
278 @MOTHUR_OVERVIEW@ 291 @MOTHUR_OVERVIEW@
279 292
280 **Command Documenation** 293 **Command Documentation**
281 294
282 The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file. 295 The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file.
283 296
284 .. _list: http://www.mothur.org/wiki/List_file 297 .. _list: https://www.mothur.org/wiki/List_file
285 .. _shared: http://www.mothur.org/wiki/Shared_file 298 .. _shared: https://www.mothur.org/wiki/Shared_file
286 .. _rabund: http://www.mothur.org/wiki/Rabund_file 299 .. _rabund: https://www.mothur.org/wiki/Rabund_file
287 .. _sabund: http://www.mothur.org/wiki/Sabund_file 300 .. _sabund: https://www.mothur.org/wiki/Sabund_file
288 .. _sub.sample: http://www.mothur.org/wiki/Sub.sample 301 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample
289 302
290 ]]> 303 ]]>
291 </help> 304 </help>
292 <expand macro="citations"/> 305 <expand macro="citations"/>
293 </tool> 306 </tool>